Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1418
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 31616
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Found at i:5039 original size:39 final size:39
Alignment explanation
Indices: 4932--5243 Score: 540
Period size: 39 Copynumber: 8.1 Consensus size: 39
4922 ATTATATTAT
* *
4932 CAGCACAAAGCCTGCGGGACTTTAACCC-GATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
4970 CAGCACGAAGCCTGC-GGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5008 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5047 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5086 CAGCACGAAGCCTGC-GGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5124 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5163 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5202 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5241 CAG
1 CAG
5244 TGTCTTGCAT
Statistics
Matches: 259, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
37 10 0.04
38 75 0.29
39 174 0.67
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:5059 original size:77 final size:78
Alignment explanation
Indices: 4932--5243 Score: 558
Period size: 77 Copynumber: 4.0 Consensus size: 78
4922 ATTATATTAT
* *
4932 CAGCACAAAGCCTGCGGGACTTTAACCC-GATACATTTCCAGCACGAAGCCTGC-GGACTTTGGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
4995 CCGGATACATTTC
66 CCGGATACATTTC
5008 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
*
5073 CCGGATATATTTC
66 CCGGATACATTTC
5086 CAGCACGAAGCCTGC-GGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
*
5150 CCGGATATATTTC
66 CCGGATACATTTC
*
5163 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
5228 CCGGATACATTTC
66 CCGGATACATTTC
5241 CAG
1 CAG
5244 TGTCTTGCAT
Statistics
Matches: 228, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
76 26 0.11
77 102 0.45
78 100 0.44
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.21
Consensus pattern (78 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGC
CCGGATACATTTC
Found at i:5135 original size:116 final size:116
Alignment explanation
Indices: 4932--5243 Score: 545
Period size: 116 Copynumber: 2.7 Consensus size: 116
4922 ATTATATTAT
* * *
4932 CAGCACAAAGCCTGCGGGACTTTAACCC-GATACATTTCCAGCACGAAGCCTGCGGACTTTGGCC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGACTTTAGCC
4996 CGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
66 CGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5047 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTCCAGCACGAAGCCTGCGGACTTTAGCC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGACTTTAGCC
* *
5112 CGGATACATTTCCAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
66 CGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5163 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGC-GGACTTTAGC
5228 CCGGATACATTTCCAG
65 CCGGATACATTTCCAG
5244 TGTCTTGCAT
Statistics
Matches: 186, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
115 25 0.13
116 135 0.73
117 26 0.14
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.21
Consensus pattern (116 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGACTTTAGCC
CGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:10192 original size:46 final size:45
Alignment explanation
Indices: 10125--10296 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 45
10115 AACCCGCCCC
* * *
10125 TAAGTGAACTCAGACTCAACTCAACAAGCTCGGGCGTTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCA
* * *
10171 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-TACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGTATCCA
* * * * *
10217 TTTCA-CGAACTCGGAATCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTATCCA
*
10264 TAAGTGAACTTGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
10297 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
45 3 0.03
46 61 0.60
47 33 0.33
48 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTATCCA
Found at i:10289 original size:93 final size:93
Alignment explanation
Indices: 10130--10300 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
10120 GCCCCTAAGT
* * * *
10130 GAACTCAGACTCAACTCAACAAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGAATCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10195 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * * *
10223 GAACTCGGAATCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCAGAATCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10288 CGAGTTCGGATGC
66 CGAGTTCGGATGC
10301 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCAGAATCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:10316 original size:46 final size:43
Alignment explanation
Indices: 10168--10308 Score: 115
Period size: 47 Copynumber: 3.1 Consensus size: 43
10158 GCGTTCGTAT
*
10168 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA
1 CCATTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---A
* * * *
10215 -CATTTCA-CGAACTCGGAATCAACTCAACGAGTTCGGACATTCGCAT
1 CCA-TT-AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAA
* *
10261 CCATAAGTGAACTTGGACTCAACTCAACGAGTTCGGATGCTCAA
1 CCATTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAA
10305 CCAT
1 CCAT
10309 CCTAGTGACA
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 29 0.39
47 30 0.40
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (43 bp):
CCATTAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAA
Found at i:14005 original size:16 final size:16
Alignment explanation
Indices: 13986--14016 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13976 CTTCTTCACT
13986 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
14002 TACTTACTTACTTAA
1 TACTCACTTACTTAA
14017 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:14022 original size:20 final size:20
Alignment explanation
Indices: 13983--14022 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13973 AAACTTCTTC
* *
13983 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
14003 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
14023 TTATTAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:14460 original size:55 final size:53
Alignment explanation
Indices: 14230--14460 Score: 224
Period size: 55 Copynumber: 4.4 Consensus size: 53
14220 ATGACTTGTT
* * * *
14230 ATGGTCTTACGTGGTATCCTT---TT-GAAACTTACCATTGCCATGTCTTGAC
1 ATGGTCTTACATGGTATCCTTGCCTTATAAACTTACCAATGCCATGCCTTGAC
* * * *
14279 ATGGTCTTACATGGTAGCCTT-CCTTATGAACTCACCAATGCCATGCCTTGGC
1 ATGGTCTTACATGGTATCCTTGCCTTATAAACTTACCAATGCCATGCCTTGAC
* * *
14331 ATGGT-TTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATGCCATGTCTTGAC
1 ATGGTCTTACATGGTATCC-TTGCCTTATA--AACTTACCAATGCCATGCCTTGAC
* * *
14385 ATGGTCTTACATGATTTCCTTGCCTTATAAACCTTACCAATTGCCATGCCTTGCC
1 ATGGTCTTACATGGTATCCTTGCCTTATAAA-CTTACCAA-TGCCATGCCTTGAC
* *
14440 ATGGCCTTACACGGTATCCTT
1 ATGGTCTTACATGGTATCCTT
14461 AAACCCTAAT
Statistics
Matches: 147, Mismatches: 24, Indels: 16
0.79 0.13 0.09
Matches are distributed among these distances:
49 19 0.13
50 2 0.01
51 13 0.09
52 31 0.21
53 2 0.01
54 32 0.22
55 46 0.31
56 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (53 bp):
ATGGTCTTACATGGTATCCTTGCCTTATAAACTTACCAATGCCATGCCTTGAC
Found at i:18589 original size:37 final size:37
Alignment explanation
Indices: 18539--18617 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
18529 TTATTACGAA
* *
18539 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
18576 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
18613 GTCTT
1 GTCTT
18618 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:18936 original size:47 final size:47
Alignment explanation
Indices: 18733--19020 Score: 415
Period size: 47 Copynumber: 6.2 Consensus size: 47
18723 CCCTTCGGGA
* * * * * * *
18733 CTTATCACATTTATGCACTTTCACATCCAT--CGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
18778 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18825 CTTA-CACATATATACACTTTCACATTCATCACATCGGCCATT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
18870 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18917 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18963 CTTATCAATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19011 CTTATCACAT
1 CTTATCACAT
19021 TCATCACATC
Statistics
Matches: 220, Mismatches: 17, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
45 32 0.15
46 80 0.36
47 102 0.46
48 6 0.03
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:19011 original size:94 final size:93
Alignment explanation
Indices: 18784--19200 Score: 445
Period size: 94 Copynumber: 4.6 Consensus size: 93
18774 CGGCCCTGTC
18784 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA-CACATATATACACTTTCAC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
*
18848 ATTCATCACATCGGCCATTGGCCTTATT
66 ATTCATCACATCGGCCATTGGCCTTATA
*
18876 ACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCAC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
*
18941 ATTCATCACATCGGCTATTAGG-CTTATCA
66 ATTCATCACATCGGCCATT-GGCCTTAT-A
*
18970 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--AT-T-CA---TCAC
1 ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
* * ** *
19028 A-TC-GC-CATTAGGCC-TTATCACATATA
66 ATTCATCACA-TCGGCCATTGGC-CTTATA
*
19054 TACACT-T-TCACA-TTCATCACA---------TCGG-CATTAGGCCTTATCACACATATACACT
1 -ACA-TATAT-ACACTT--TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
*
19106 TTCACATTCATCACATCGGCCATTAGGCCTTATC
61 TTCACATTCATCACATCGGCCATT-GGCCTTATA
*
19140 ACATATATACACTTTCACATTCATCATCATCGGCTATTAGGCCTTATCACATATATACACT
1 ACATATATACACTTTCACATTCATCA-CATCGGCCATTAGGCCTTATCACATATATACACT
19201 GTCTTGGCTG
Statistics
Matches: 268, Mismatches: 20, Indels: 71
0.75 0.06 0.20
Matches are distributed among these distances:
76 16 0.06
77 4 0.01
78 2 0.01
79 1 0.00
80 2 0.01
83 5 0.02
84 16 0.06
85 28 0.10
86 19 0.07
87 6 0.02
90 2 0.01
91 1 0.00
92 46 0.17
93 42 0.16
94 53 0.20
95 25 0.09
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (93 bp):
ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCAC
ATTCATCACATCGGCCATTGGCCTTATA
Found at i:19037 original size:30 final size:31
Alignment explanation
Indices: 18984--19050 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
18974 ATATACACTT
18984 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
19015 TCACATTCATCACATC-GCCATTAGGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
19045 TCACAT
1 TCACAT
19051 ATATACACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (31 bp):
TCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:19054 original size:171 final size:171
Alignment explanation
Indices: 18844--19191 Score: 603
Period size: 171 Copynumber: 2.0 Consensus size: 171
18834 ATATACACTT
*
18844 TCACATTCATCACATCGGCCATTGGCCTTATTACATATATACACTTTCACATTCATCACATCGGC
1 TCACATTCATCACATCGGCCATTGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
* * *
18909 TATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGG-CTTATCAATA
66 -ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC-ACA
18973 TATATACACTTTCACATTCATCA-CATCGGCCATTAGGCCTTA
129 TATATACACTTTCACATTCATCATCATCGGCCATTAGGCCTTA
19015 TCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATT-GGCCTTATCACATATATACACTTTCACATTCATCACATCGG
19079 CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
65 CATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
19144 ATATACACTTTCACATTCATCATCATCGGCTATTAGGCCTTA
130 ATATACACTTTCACATTCATCATCATCGGCCATTAGGCCTTA
19186 TCACAT
1 TCACAT
19192 ATATACACTG
Statistics
Matches: 169, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
170 82 0.49
171 87 0.51
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (171 bp):
TCACATTCATCACATCGGCCATTGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
ATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
TATACACTTTCACATTCATCATCATCGGCCATTAGGCCTTA
Found at i:19065 original size:77 final size:77
Alignment explanation
Indices: 18937--19095 Score: 268
Period size: 77 Copynumber: 2.1 Consensus size: 77
18927 ATATACACTT
* *
18937 TCACATTCATCACATCGGCTATTAGGCTTATCAATATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCTTATCAACATATATACACTTTCACATTCATCACATCGG
19002 CCATTAGGCCTTA
66 -CATTAGGCCTTA
19015 TCACATTCATCACATC-GCCATTAGGCCTTATC-ACATATATACACTTTCACATTCATCACATCG
1 TCACATTCATCACATCGGCCATTAGG-CTTATCAACATATATACACTTTCACATTCATCACATCG
19078 GCATTAGGCCTTA
65 GCATTAGGCCTTA
19091 TCACA
1 TCACA
19096 CATATACACT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
76 17 0.22
77 39 0.50
78 22 0.28
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (77 bp):
TCACATTCATCACATCGGCCATTAGGCTTATCAACATATATACACTTTCACATTCATCACATCGG
CATTAGGCCTTA
Found at i:19189 original size:48 final size:47
Alignment explanation
Indices: 19015--19200 Score: 331
Period size: 46 Copynumber: 4.0 Consensus size: 47
19005 TTAGGCCTTA
19015 TCACATTCATCACATC-GCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
*
19061 TCACATTCATCACATCGG-CATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
19107 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
*
19154 TCACATTCATCATCATCGGCTATTAGGCCTTATCACATATATACACT
1 TCACATTCATCA-CATCGGCCATTAGGCCTTATCACATATATACACT
19201 GTCTTGGCTG
Statistics
Matches: 134, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
46 61 0.46
47 40 0.30
48 33 0.25
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
Found at i:22753 original size:40 final size:40
Alignment explanation
Indices: 22706--22884 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
22696 CAGCATGATG
* * *
22706 ATGCTCTTCGGGACCTAGCCCGGATAT-TACACCAGCACGA
1 ATGCTCTTCGGAACTTAGCCCGGATATAT-CACTAGCACGA
*** *
22746 ATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGA
1 ATGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGA
* * *
22786 ATGCTCTTCGGAACTTAGTCCAGATACATCACTAGCACGA
1 ATGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGA
* *
22826 ATGCTCTTCGGAACTTAGTCCGGATATGGTCACTAGCAC-A
1 ATGCTCTTCGGAACTTAGCCCGGATAT-ATCACTAGCACGA
* *
22866 A-ACCCTTCGG-ACTTAGCCC
1 ATGCTCTTCGGAACTTAGCCC
22885 AGCATCATTC
Statistics
Matches: 119, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 8 0.07
39 7 0.06
40 93 0.78
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
ATGCTCTTCGGAACTTAGCCCGGATATATCACTAGCACGA
Found at i:23227 original size:29 final size:29
Alignment explanation
Indices: 23195--23268 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
23185 TAATCAACCA
* * *
23195 CGCACACTTAGTGCCATGTACTTTTAA-CT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCC
23224 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAGCC
23253 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
23269 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCC
Found at i:23342 original size:42 final size:43
Alignment explanation
Indices: 23250--23351 Score: 188
Period size: 43 Copynumber: 2.4 Consensus size: 43
23240 TGCATTTCAA
23250 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
*
23293 GCTCGCACACTTAGTGCCAATCTCACAACC-TGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
23335 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
23352 TGAAAACCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 28 0.49
43 29 0.51
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
Found at i:29127 original size:49 final size:48
Alignment explanation
Indices: 29034--29468 Score: 250
Period size: 48 Copynumber: 9.3 Consensus size: 48
29024 AGCCCAAGAC
29034 AGTGTATATATGTGATAAGGCCT-AT-AGCCAGATG-TGATTG-ATGTGAA
1 AGTGTATATATGTGATAA-GCCTAATGAGCC-GATGTTGA-TGAATGTGAA
29081 AGTGGTATATAT-TGCACTAAGCCTAATGAGCCGATG-TGATGAATGTGAA
1 AGT-GTATATATGTG-A-TAAGCCTAATGAGCCGATGTTGATGAATGTGAA
*
29130 AGTCGTATATGTGTGATAAGGCCTAAT-A-CCGATGTTGATGAATGTGAA
1 AGT-GTATATATGTGATAA-GCCTAATGAGCCGATGTTGATGAATGTGAA
29178 GAGTGTATATATGTGAATAAGCGCTACATG-GCCGA-GTTGATGAATGTG-A
1 -AGTGTATATATGTG-ATAAGC-CTA-ATGAGCCGATGTTGATGAATGTGAA
* **
29227 A---TATA-ATCTCTTAA---T-A-G-GCCGATGTTTGATGAATGTGAA
1 AGTGTATATATGTGATAAGCCTAATGAGCCGATG-TTGATGAATGTGAA
*
29266 A-TCGTTATATATTATTG-TAAG-CTAA--AGCCCAGATG-TGATGAATGTGAA
1 AGT-G-TATATA-T-GTGATAAGCCTAATGAG-CC-GATGTTGATGAATGTGAA
29314 AGTGGTAT-TATGTGAATTAAGGCCCTAAT-AGCCGATG-TGATGAATGTGAA
1 AGT-GTATATATGTG-A-TAA-G-CCTAATGAGCCGATGTTGATGAATGTGAA
* *
29364 AGTGT-TATAT-TAATAAGGCTAATG-GCC-ATG-TGATGAATGTGAA
1 AGTGTATATATGTGATAAGCCTAATGAGCCGATGTTGATGAATGTGAA
*
29407 AG-GTAGTAT-TGTG-TAAGGCCTAATG-GCCAATG-TGATGATATTGTGAA
1 AGTGTA-TATATGTGATAA-GCCTAATGAGCCGATGTTGATGA-A-TGTGAA
29454 AGT-TATCATATGTGA
1 AGTGTAT-ATATGTGA
29469 CAGGGCCGAG
Statistics
Matches: 322, Mismatches: 14, Indels: 102
0.74 0.03 0.23
Matches are distributed among these distances:
36 6 0.02
37 2 0.01
38 12 0.04
39 3 0.01
42 2 0.01
43 29 0.09
44 26 0.08
45 20 0.06
46 7 0.02
47 27 0.08
48 73 0.23
49 58 0.18
50 45 0.14
51 10 0.03
52 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (48 bp):
AGTGTATATATGTGATAAGCCTAATGAGCCGATGTTGATGAATGTGAA
Found at i:29219 original size:50 final size:49
Alignment explanation
Indices: 29074--29227 Score: 160
Period size: 49 Copynumber: 3.1 Consensus size: 49
29064 GATGTGATTG
* *
29074 ATGTGAAAGTGGTATATAT-TGCACTAAGC-CTAATGAGCCGA-TGTGATGA
1 ATGTGAAAGTCGTATATATGTG-AATAAGCGCTAATG-GCCGAGT-TGATGA
* *
29123 ATGTGAAAGTCGTATATGTGTG-ATAAG-GCCTAAT-ACCGATGTTGATGA
1 ATGTGAAAGTCGTATATATGTGAATAAGCG-CTAATGGCCGA-GTTGATGA
29171 ATGTGAAGAGT-GTATATATGTGAATAAGCGCTACATGGCCGAGTTGATGA
1 ATGTGAA-AGTCGTATATATGTGAATAAGCGCTA-ATGGCCGAGTTGATGA
29221 ATGTGAA
1 ATGTGAA
29228 TATAATCTCT
Statistics
Matches: 89, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
47 4 0.04
48 27 0.30
49 34 0.38
50 20 0.22
51 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.29
Consensus pattern (49 bp):
ATGTGAAAGTCGTATATATGTGAATAAGCGCTAATGGCCGAGTTGATGA
Found at i:29395 original size:43 final size:46
Alignment explanation
Indices: 29298--29456 Score: 175
Period size: 43 Copynumber: 3.4 Consensus size: 46
29288 TAAAGCCCAG
* * *
29298 ATGTGATGAATGTGAAAGTGGTATTATGTGAATTAAGGCCCTAATAGCCG
1 ATGTGATGAATGTGAAAGT-GTAGTAT-TGAA-TAAGG-CCTAATGGCCA
29348 ATGTGATGAATGTGAAAGTGTTA-TATT-AATAAGG-CTAATGGCC-
1 ATGTGATGAATGTGAAAGTG-TAGTATTGAATAAGGCCTAATGGCCA
**
29391 ATGTGATGAATGTGAAAG-GTAGTATTGTGTAAGGCCTAATGGCCA
1 ATGTGATGAATGTGAAAGTGTAGTATTGAATAAGGCCTAATGGCCA
29436 ATGTGATGATATTGTGAAAGT
1 ATGTGATGA-A-TGTGAAAGT
29457 TATCATATGT
Statistics
Matches: 98, Mismatches: 3, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
41 2 0.02
42 5 0.05
43 23 0.23
44 17 0.17
45 9 0.09
46 6 0.06
47 10 0.10
48 1 0.01
49 4 0.04
50 21 0.21
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (46 bp):
ATGTGATGAATGTGAAAGTGTAGTATTGAATAAGGCCTAATGGCCA
Done.